5VRL | pdb_00005vrl

CRYSTAL STRUCTURE OF THE INHA FROM MYCOBACTERIUM TUBERCULOSIS IN COMPLEX WITH AN12855, EBSI 4333.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 
    0.198 (Depositor), 0.203 (DCC) 
  • R-Value Work: 
    0.172 (Depositor), 0.187 (DCC) 
  • R-Value Observed: 
    0.173 (Depositor) 

wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Discovery of a cofactor-independent inhibitor ofMycobacterium tuberculosisInhA.

Xia, Y.Zhou, Y.Carter, D.S.McNeil, M.B.Choi, W.Halladay, J.Berry, P.W.Mao, W.Hernandez, V.O'Malley, T.Korkegian, A.Sunde, B.Flint, L.Woolhiser, L.K.Scherman, M.S.Gruppo, V.Hastings, C.Robertson, G.T.Ioerger, T.R.Sacchettini, J.Tonge, P.J.Lenaerts, A.J.Parish, T.Alley, M.

(2018) Life Sci Alliance 1: e201800025-e201800025

  • DOI: https://doi.org/10.26508/lsa.201800025
  • Primary Citation Related Structures: 
    5VRL, 5VRM, 5VRN

  • PubMed Abstract: 

    New antitubercular agents are needed to combat the spread of multidrug- and extensively drug-resistant strains of Mycobacterium tuberculosis . The frontline antitubercular drug isoniazid (INH) targets the mycobacterial enoyl-ACP reductase, InhA. Resistance to INH is predominantly through mutations affecting the prodrug-activating enzyme KatG. Here, we report the identification of the diazaborines as a new class of direct InhA inhibitors. The lead compound, AN12855, exhibited in vitro bactericidal activity against replicating bacteria and was active against several drug-resistant clinical isolates. Biophysical and structural investigations revealed that AN12855 binds to and inhibits the substrate-binding site of InhA in a cofactor-independent manner. AN12855 showed good drug exposure after i.v. and oral delivery, with 53% oral bioavailability. Delivered orally, AN12855 exhibited dose-dependent efficacy in both an acute and chronic murine model of tuberculosis infection that was comparable with INH. Combined, AN12855 is a promising candidate for the development of new antitubercular agents.


  • Organizational Affiliation
    • Anacor Pharmaceuticals, Palo Alto, CA, USA.

Macromolecule Content 

  • Total Structure Weight: 29.3 kDa 
  • Atom Count: 1,995 
  • Modeled Residue Count: 264 
  • Deposited Residue Count: 272 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Enoyl-[acyl-carrier-protein] reductase [NADH]272Mycobacterium tuberculosis CDC1551Mutation(s): 0 
Gene Names: inhAMT1531
EC: 1.3.1.9
UniProt
Find proteins for P9WGR1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WGR1 
Go to UniProtKB:  P9WGR1
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WGR1
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
9JA

Query on 9JA



Download:Ideal Coordinates CCD File
B [auth A](~{N}~{E})-~{N}-[[2-[[2-ethylsulfonyl-1,1-bis(oxidanyl)-3,4-dihydro-2,3,1$l^{4}-benzodiazaborinin-7-yl]oxy]-5-(trifluoromethyl)phenyl]methylidene]hydroxylamine
C17 H18 B F3 N3 O6 S
MTDIXAKABVYTBV-AUEPDCJTSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free:  0.198 (Depositor), 0.203 (DCC) 
  • R-Value Work:  0.172 (Depositor), 0.187 (DCC) 
  • R-Value Observed: 0.173 (Depositor) 
Space Group: I 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.08α = 90
b = 94.08β = 90
c = 184.43γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Bill & Melinda Gates FoundationUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2018-05-16
    Type: Initial release
  • Version 1.1: 2018-11-21
    Changes: Data collection, Database references
  • Version 1.2: 2018-12-05
    Changes: Data collection, Database references
  • Version 1.3: 2024-03-13
    Changes: Data collection, Database references